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imagej-elphel
Commit 227c8f63 authored by Andrey Filippov's avatar Andrey Filippov
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More filtering modes

parent 3a766b8e
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Showing with 493 additions and 170 deletions
pom.xml
View file @ 227c8f63
......@@ -78,9 +78,8 @@
<artifactId>maven-plugin-plugin</artifactId>
<configuration>
<!-- see http://jira.codehaus.org/browse/MNG-5346 -->
<skipErrorNoDescriptorsFound>true</skipErrorNoDescriptorsFound>
<skipErrorNoDescriptorsFound>true</skipErrorNoDescriptorsFound>
</configuration>
<executions>
<execution>
<id>mojo-descriptor</id>
......@@ -89,6 +88,7 @@
</goals>
</execution>
</executions>
</plugin>
<plugin>
......
src/main/java/Aberration_Calibration.java
View file @ 227c8f63
......@@ -796,6 +796,7 @@ if (MORE_BUTTONS) {
addButton("Scan Calib LMA", panelCurvature,color_process);
addButton("Save History", panelCurvature,color_debug);
addButton("Restore History",panelCurvature,color_restore);
addButton("History RMS", panelCurvature,color_report);
addButton("Modify LMA", panelCurvature,color_configure);
addButton("Load strategies", panelCurvature,color_restore);
addButton("Organize strategies", panelCurvature,color_configure);
......@@ -4088,7 +4089,12 @@ if (MORE_BUTTONS) {
FOCUSING_FIELD.saveXML(path);
saveCurrentConfig();
// for now just copying from "Restore History". TODO: Make both more automatic (move number of parameters outside?)
if (!FOCUSING_FIELD.configureDataVector("Configure curvature - TODO: fix many settings restored from properties",true,true)) return;
if (!FOCUSING_FIELD.configureDataVector(
true, //boolean silent
"Configure curvature - TODO: fix many settings restored from properties", // String title,
true, //boolean forcenew
true) // boolean enableReset
) return;
System.out.println("TODO: fix many settings restored from properties, overwriting entered fields. Currently run \"Modify LMA\" to re-enter values");
System.out.println("TODO: Probably need to make a separate dialog that enters number of parameters.");
double [] sv= FOCUSING_FIELD.fieldFitting.createParameterVector(FOCUSING_FIELD.sagittalMaster);
......@@ -4419,7 +4425,12 @@ if (MORE_BUTTONS) {
FOCUSING_FIELD.setAdjustMode(false);
if (PROPERTIES!=null) FOCUSING_FIELD.getProperties("FOCUSING_FIELD.", PROPERTIES);
System.out.println("Loaded FocusingField");
if (!FOCUSING_FIELD.configureDataVector("Configure curvature - TODO: fix many settings restored from properties",true,true)) return;
if (!FOCUSING_FIELD.configureDataVector(
true, // boolean silent (maybe add option with false to change number of parameters?)
"Configure curvature - TODO: fix many settings restored from properties", // String title
true, // boolean forcenew,
true) // boolean enableReset
) return;
System.out.println("TODO: fix many settings restored from properties, overwriting entered fields. Currently run \"Modify LMA\" to re-enter values");
System.out.println("TODO: Probably need to make a separate dialog that enters number of parameters.");
double [] sv= FOCUSING_FIELD.fieldFitting.createParameterVector(FOCUSING_FIELD.sagittalMaster);
......@@ -4432,13 +4443,35 @@ if (MORE_BUTTONS) {
System.out.println("rms="+rms+", rms_pure="+rms_pure);
return;
}
/* ======================================================================== */
if (label.equals("History RMS")) {
if (FOCUSING_FIELD==null) return;
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
// FOCUSING_FIELD.setAdjustMode(false);
double [] sv= FOCUSING_FIELD.fieldFitting.createParameterVector(FOCUSING_FIELD.sagittalMaster);
FOCUSING_FIELD.setDataVector(
true, // calibrate mode
FOCUSING_FIELD.createDataVector());
double [] focusing_fx= FOCUSING_FIELD.createFXandJacobian(sv, false);
double rms= FOCUSING_FIELD.calcErrorDiffY(focusing_fx, false);
double rms_pure= FOCUSING_FIELD.calcErrorDiffY(focusing_fx, true);
System.out.println("rms="+rms+", rms_pure="+rms_pure);
FOCUSING_FIELD.printSetRMS(focusing_fx);
return;
}
/* ======================================================================== */
if (label.equals("Modify LMA")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
if (FOCUSING_FIELD==null) return;
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
FOCUSING_FIELD.setAdjustMode(false);
if (!FOCUSING_FIELD.configureDataVector("Re-configure curvature parameters",false,true)) return;
if (!FOCUSING_FIELD.configureDataVector(
false, // boolean silent,
"Re-configure curvature parameters", // String title
false, // boolean forcenew
true) // boolean enableReset
) return;
FOCUSING_FIELD.setDataVector(
true, // calibrate mode
FOCUSING_FIELD.createDataVector());
......
src/main/java/FocusingField.java
View file @ 227c8f63
......@@ -85,6 +85,10 @@ public class FocusingField {
double filterTiltedByValueScale; // filter tilted measurement samples if the spot FWHM is higher than scaled best FWHM
boolean filterByScanValue; // filter adjustment samples if fwhm exceeds maximal used in focal scan mode
boolean filterTiltedByScanValue; // filter tilted samples if fwhm exceeds maximal used in focal scan mode
int filterByNeib; // remove samples having less neighbors (same channel) that this during adjustment
int filterCalibByNeib; // remove samples having less neighbors (same channel) that this during calibration
double filterSetsByRMS; // remove complete sets (same timestamp) with RMS greater than scaled average
boolean filterSetsByRMSTiltOnly; // only remove non-scan sets
int minLeftSamples; // minimal number of samples (channel/dir/location) for adjustment
int minCenterSamplesBest; // minimal number of samples (channel/dir/location) for adjustment in the center, best channel
int minCenterSamplesTotal; // minimal number of samples (channel/dir/location) for adjustment in the center, all channels total
......@@ -238,7 +242,11 @@ public class FocusingField {
filterTiltedByValueScale=1.5;
filterByScanValue=true; // filter adjustment samples if fwhm exceeds maximal used in focal scan mode
filterTiltedByScanValue=true; // filter tilted samples if fwhm exceeds maximal used in focal scan mode
filterByNeib=3; // remove samples having less neighbors (same channel) that this during adjustment
filterCalibByNeib=3; // remove samples having less neighbors (same channel) that this during calibration
filterSetsByRMS=0.0; // remove complete sets (same timestamp) with RMS greater than scaled average
filterSetsByRMSTiltOnly=true; // only remove non-scan sets
minLeftSamples=10; // minimal number of samples (channel/dir/location) for adjustment
minCenterSamplesBest=4; // minimal number of samples (channel/dir/location) for adjustment in the center, best channel
minCenterSamplesTotal=0;// minimal number of samples (channel/dir/location) for adjustment in the center, all channels total
......@@ -377,6 +385,10 @@ public class FocusingField {
properties.setProperty(prefix+"filterTiltedByValueScale",filterTiltedByValueScale+"");
properties.setProperty(prefix+"filterByScanValue",filterByScanValue+"");
properties.setProperty(prefix+"filterTiltedByScanValue",filterTiltedByScanValue+"");
properties.setProperty(prefix+"filterByNeib",filterByNeib+"");
properties.setProperty(prefix+"filterCalibByNeib",filterCalibByNeib+"");
properties.setProperty(prefix+"filterSetsByRMS",filterSetsByRMS+"");
properties.setProperty(prefix+"filterSetsByRMSTiltOnly",filterSetsByRMSTiltOnly+"");
properties.setProperty(prefix+"minLeftSamples",minLeftSamples+"");
properties.setProperty(prefix+"minCenterSamplesBest",minCenterSamplesBest+"");
properties.setProperty(prefix+"minCenterSamplesTotal",minCenterSamplesTotal+"");
......@@ -491,6 +503,14 @@ public class FocusingField {
filterByScanValue=Boolean.parseBoolean(properties.getProperty(prefix+"filterByScanValue"));
if (properties.getProperty(prefix+"filterTiltedByScanValue")!=null)
filterTiltedByScanValue=Boolean.parseBoolean(properties.getProperty(prefix+"filterTiltedByScanValue"));
if (properties.getProperty(prefix+"filterByNeib")!=null)
filterByNeib=Integer.parseInt(properties.getProperty(prefix+"filterByNeib"));
if (properties.getProperty(prefix+"filterCalibByNeib")!=null)
filterCalibByNeib=Integer.parseInt(properties.getProperty(prefix+"filterCalibByNeib"));
if (properties.getProperty(prefix+"filterSetsByRMS")!=null)
filterSetsByRMS=Double.parseDouble(properties.getProperty(prefix+"filterSetsByRMS"));
if (properties.getProperty(prefix+"filterSetsByRMSTiltOnly")!=null)
filterSetsByRMSTiltOnly=Boolean.parseBoolean(properties.getProperty(prefix+"filterSetsByRMSTiltOnly"));
if (properties.getProperty(prefix+"minLeftSamples")!=null)
minLeftSamples=Integer.parseInt(properties.getProperty(prefix+"minLeftSamples"));
if (properties.getProperty(prefix+"minCenterSamplesBest")!=null)
......@@ -686,139 +706,158 @@ public class MeasuredSample{
this.scan=scan;
}
}
public boolean configureDataVector(String title, boolean forcenew, boolean enableReset){
if ((fieldFitting == null) && !forcenew){
forcenew=true;
}
boolean setupMasks=true,setupParameters=true,showDisabled=true;
FieldFitting tmpFieldFitting=fieldFitting;
if (tmpFieldFitting==null) tmpFieldFitting= new FieldFitting(); // just to get field description
int [] numCurvPars=tmpFieldFitting.getNumCurvars();
GenericDialog gd = new GenericDialog(title+(forcenew?" RESETTING DATA":""));
gd.addCheckbox("Only use measurements acquired during parallel moves (false - use all)",parallelOnly);
gd.addCheckbox("Remove \"crazy\" input data (small motor move causing large variations of FWHM)",filterInput);
gd.addNumericField("Maximal motor move to be considered small",filterInputMotorDiff,0,5,"steps (~90um/step)");
gd.addNumericField("Maximal allowed PSF FWHM variations fro the move above",filterInputDiff,3,5,"um");
gd.addCheckbox("Remove first/last in a series of measuremnts separated by small (see above) steps",filterInputFirstLast);
gd.addCheckbox("Remove measurements taken too far from the rest for the same channel/sample",filterInputTooFar);
gd.addNumericField("\"Too far\" ratio to the average distance to the center of measurements",filterInputFarRatio,3,5,"um");
gd.addCheckbox("Filter non-concave areas from best focus for each sample",filterInputConcave);
gd.addNumericField("Concave filter sigma",filterInputConcaveSigma,3,5,"um");
gd.addCheckbox("Remove small series ",filterInputConcaveRemoveFew);
gd.addNumericField("Minimal number of samples (to remove / apply concave filter) ",filterInputConcaveMinSeries,3,5,"samples");
gd.addNumericField("Concave filter scale",filterInputConcaveScale,3,5,"<=1.0");
gd.addCheckbox("Filter tilted samples/channels by Z",filterTiltedZ);
gd.addCheckbox("Filter tilted samples by value (leave lower than maximal fwhm used in focal scan mode)",filterTiltedByScanValue);
gd.addNumericField("Filter tilted samples by value (remove samples above scaled best FWHM for channel/location)",filterTiltedByValueScale,2,5,"x");
gd.addCheckbox("Sagittal channels are master channels (false - tangential are masters)",sagittalMaster);
gd.addMessage("=== Setting minimal measured PSF radius for different colors/directions ===");
for (int i=0;i<minMeas.length;i++){
gd.addNumericField(tmpFieldFitting.getDescription(i),this.minMeas[i],3,5,"pix");
}
gd.addCheckbox("Use minimal radius",useMinMeas);
gd.addMessage("=== Setting maximal measured PSF radius for different colors/directions ===");
for (int i=0;i<maxMeas.length;i++){
gd.addNumericField(tmpFieldFitting.getDescription(i),this.maxMeas[i],3,5,"pix");
}
gd.addCheckbox("Use maximal radius",useMaxMeas);
gd.addMessage("=== Setting maximal usable PSF radius for different colors/directions ===");
for (int i=0;i<thresholdMax.length;i++){
gd.addNumericField(tmpFieldFitting.getDescription(i),this.thresholdMax[i],3,5,"pix");
}
gd.addCheckbox("Discard measurements with PSF radius above specified above threshold",useThresholdMax);
if (forcenew) {
gd.addMessage("=== Setting number of parameters for approximation of the PSF dimensions ===");
gd.addNumericField("Number of parameters for psf(z) approximation (>=3)",numCurvPars[0],0);
gd.addNumericField("Number of parameters for radial dependence of PSF curves (>=1)",numCurvPars[1],0);
}
gd.addMessage("");
gd.addNumericField("Data weight mode (0 - equal mode, 1 -linear treshold diff, 2 - quadratic threshold diff)",weightMode,0);
gd.addNumericField("Data weight radius (multiply weight by Gaussian), 0 - no dependence on radius",weightRadius,3,5,"mm");
gd.addCheckbox("Setup parameter masks?",setupMasks);
gd.addCheckbox("Setup parameter values?",setupParameters);
gd.addCheckbox("Show/modify disabled for auto-adjustment parameters?",showDisabled);
gd.addCheckbox("Debug feature: update measurements and /dxc, /dyc if center is being fitted",correct_measurement_ST);
gd.addCheckbox("Debug feature: update sample weights during fitting",updateWeightWhileFitting);
if (enableReset) gd.enableYesNoCancel("OK","Reset to defaults, re-open"); // default OK (on enter) - "Apply"
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return false;
if (!gd.wasOKed()) {
savedProperties=null;
setDefaults();
if (!configureDataVector(title, true,false)) return false;
return true;
}
// boolean configureDataVector(String title, boolean forcenew, boolean moreset)
parallelOnly= gd.getNextBoolean();
filterInput= gd.getNextBoolean();
filterInputMotorDiff= gd.getNextNumber();
filterInputDiff= gd.getNextNumber();
filterInputFirstLast= gd.getNextBoolean();
filterInputTooFar= gd.getNextBoolean();
filterInputFarRatio= gd.getNextNumber();
filterInputConcave= gd.getNextBoolean();
filterInputConcaveSigma= gd.getNextNumber();
filterInputConcaveRemoveFew= gd.getNextBoolean();
filterInputConcaveMinSeries= (int) gd.getNextNumber();
filterInputConcaveScale= gd.getNextNumber();
filterTiltedZ= gd.getNextBoolean();
filterTiltedByScanValue= gd.getNextBoolean();
filterTiltedByValueScale= gd.getNextNumber();
sagittalMaster= gd.getNextBoolean();
for (int i=0;i<minMeas.length;i++)this.minMeas[i]= gd.getNextNumber();
useMinMeas= gd.getNextBoolean();
for (int i=0;i<maxMeas.length;i++) this.maxMeas[i]= gd.getNextNumber();
useMaxMeas= gd.getNextBoolean();
for (int i=0;i<thresholdMax.length;i++) this.thresholdMax[i] = gd.getNextNumber();
useThresholdMax= gd.getNextBoolean();
if (forcenew) {
numCurvPars[0] = (int) gd.getNextNumber();
numCurvPars[1] = (int) gd.getNextNumber();
}
weightMode = (int) gd.getNextNumber();
weightRadius = gd.getNextNumber();
setupMasks= gd.getNextBoolean();
setupParameters= gd.getNextBoolean();
showDisabled= gd.getNextBoolean();
correct_measurement_ST= gd.getNextBoolean();
updateWeightWhileFitting= gd.getNextBoolean();
if (forcenew) {
this.fieldFitting= new FieldFitting(
currentPX0,
currentPY0,
numCurvPars[0],
numCurvPars[1]);
if (savedProperties!=null){
if (debugLevel>0) System.out.println("configureDataVector(): Applying properties");
getProperties(propertiesPrefix,savedProperties); // overwrites parallelOnly!
}
}
public boolean configureDataVector(
boolean silent,
String title,
boolean forcenew,
boolean enableReset){
if ((fieldFitting == null) && !forcenew){
forcenew=true;
}
boolean setupMasks=silent?false:true;
boolean setupParameters=silent?false:true;
boolean showDisabled=silent?false:true;
FieldFitting tmpFieldFitting=fieldFitting;
if (tmpFieldFitting==null) tmpFieldFitting= new FieldFitting(); // just to get field description
int [] numCurvPars=tmpFieldFitting.getNumCurvars();
if (!silent) {
GenericDialog gd = new GenericDialog(title+(forcenew?" RESETTING DATA":""));
gd.addCheckbox("Only use measurements acquired during parallel moves (false - use all)",parallelOnly);
gd.addCheckbox("Remove \"crazy\" input data (small motor move causing large variations of FWHM)",filterInput);
gd.addNumericField("Maximal motor move to be considered small",filterInputMotorDiff,0,5,"steps (~90um/step)");
gd.addNumericField("Maximal allowed PSF FWHM variations fro the move above",filterInputDiff,3,5,"um");
gd.addCheckbox("Remove first/last in a series of measuremnts separated by small (see above) steps",filterInputFirstLast);
gd.addCheckbox("Remove measurements taken too far from the rest for the same channel/sample",filterInputTooFar);
gd.addNumericField("\"Too far\" ratio to the average distance to the center of measurements",filterInputFarRatio,3,5,"um");
gd.addCheckbox("Filter non-concave areas from best focus for each sample",filterInputConcave);
gd.addNumericField("Concave filter sigma",filterInputConcaveSigma,3,5,"um");
gd.addCheckbox("Remove small series ",filterInputConcaveRemoveFew);
gd.addNumericField("Minimal number of samples (to remove / apply concave filter) ",filterInputConcaveMinSeries,3,5,"samples");
gd.addNumericField("Concave filter scale",filterInputConcaveScale,3,5,"<=1.0");
gd.addCheckbox("Filter tilted samples/channels by Z",filterTiltedZ);
gd.addCheckbox("Filter tilted samples by value (leave lower than maximal fwhm used in focal scan mode)",filterTiltedByScanValue);
gd.addNumericField("Filter tilted samples by value (remove samples above scaled best FWHM for channel/location)",filterTiltedByValueScale,2,5,"x");
gd.addNumericField("Remove samples having less neighbors (same channel) than this",filterCalibByNeib,0,1,"");
gd.addNumericField("Remove complete sets (same timestamp) with RMS greater than scaled average RMS",filterSetsByRMS,3,5,"x");
gd.addCheckbox("Only remove sets of tilt calibration, keep focus scanning ones",filterSetsByRMSTiltOnly);
gd.addCheckbox("Sagittal channels are master channels (false - tangential are masters)",sagittalMaster);
gd.addMessage("=== Setting minimal measured PSF radius for different colors/directions ===");
for (int i=0;i<minMeas.length;i++){
gd.addNumericField(tmpFieldFitting.getDescription(i),this.minMeas[i],3,5,"pix");
}
gd.addCheckbox("Use minimal radius",useMinMeas);
gd.addMessage("=== Setting maximal measured PSF radius for different colors/directions ===");
for (int i=0;i<maxMeas.length;i++){
gd.addNumericField(tmpFieldFitting.getDescription(i),this.maxMeas[i],3,5,"pix");
}
gd.addCheckbox("Use maximal radius",useMaxMeas);
gd.addMessage("=== Setting maximal usable PSF radius for different colors/directions ===");
for (int i=0;i<thresholdMax.length;i++){
gd.addNumericField(tmpFieldFitting.getDescription(i),this.thresholdMax[i],3,5,"pix");
}
gd.addCheckbox("Discard measurements with PSF radius above specified above threshold",useThresholdMax);
if (forcenew) {
gd.addMessage("=== Setting number of parameters for approximation of the PSF dimensions ===");
gd.addNumericField("Number of parameters for psf(z) approximation (>=3)",numCurvPars[0],0);
gd.addNumericField("Number of parameters for radial dependence of PSF curves (>=1)",numCurvPars[1],0);
}
gd.addMessage("");
gd.addNumericField("Data weight mode (0 - equal mode, 1 -linear treshold diff, 2 - quadratic threshold diff)",weightMode,0);
gd.addNumericField("Data weight radius (multiply weight by Gaussian), 0 - no dependence on radius",weightRadius,3,5,"mm");
gd.addCheckbox("Setup parameter masks?",setupMasks);
gd.addCheckbox("Setup parameter values?",setupParameters);
gd.addCheckbox("Show/modify disabled for auto-adjustment parameters?",showDisabled);
gd.addCheckbox("Debug feature: update measurements and /dxc, /dyc if center is being fitted",correct_measurement_ST);
gd.addCheckbox("Debug feature: update sample weights during fitting",updateWeightWhileFitting);
if (enableReset) gd.enableYesNoCancel("OK","Reset to defaults, re-open"); // default OK (on enter) - "Apply"
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return false;
if (!gd.wasOKed()) {
savedProperties=null;
setDefaults();
if (!configureDataVector(false,title, true,false)) return false;
return true;
}
// boolean configureDataVector(String title, boolean forcenew, boolean moreset)
parallelOnly= gd.getNextBoolean();
filterInput= gd.getNextBoolean();
filterInputMotorDiff= gd.getNextNumber();
filterInputDiff= gd.getNextNumber();
filterInputFirstLast= gd.getNextBoolean();
filterInputTooFar= gd.getNextBoolean();
filterInputFarRatio= gd.getNextNumber();
filterInputConcave= gd.getNextBoolean();
filterInputConcaveSigma= gd.getNextNumber();
filterInputConcaveRemoveFew= gd.getNextBoolean();
filterInputConcaveMinSeries= (int) gd.getNextNumber();
filterInputConcaveScale= gd.getNextNumber();
filterTiltedZ= gd.getNextBoolean();
filterTiltedByScanValue= gd.getNextBoolean();
filterTiltedByValueScale= gd.getNextNumber();
filterCalibByNeib= (int) gd.getNextNumber();
filterSetsByRMS= gd.getNextNumber();
filterSetsByRMSTiltOnly= gd.getNextBoolean();
sagittalMaster= gd.getNextBoolean();
for (int i=0;i<minMeas.length;i++)this.minMeas[i]= gd.getNextNumber();
useMinMeas= gd.getNextBoolean();
for (int i=0;i<maxMeas.length;i++) this.maxMeas[i]= gd.getNextNumber();
useMaxMeas= gd.getNextBoolean();
for (int i=0;i<thresholdMax.length;i++) this.thresholdMax[i] = gd.getNextNumber();
useThresholdMax= gd.getNextBoolean();
if (forcenew) {
numCurvPars[0] = (int) gd.getNextNumber();
numCurvPars[1] = (int) gd.getNextNumber();
}
weightMode = (int) gd.getNextNumber();
weightRadius = gd.getNextNumber();
setupMasks= gd.getNextBoolean();
setupParameters= gd.getNextBoolean();
showDisabled= gd.getNextBoolean();
correct_measurement_ST= gd.getNextBoolean();
updateWeightWhileFitting= gd.getNextBoolean();
}
if (forcenew) {
this.fieldFitting= new FieldFitting(
currentPX0,
currentPY0,
numCurvPars[0],
numCurvPars[1]);
if (savedProperties!=null){
if (debugLevel>0) System.out.println("configureDataVector(): Applying properties");
getProperties(propertiesPrefix,savedProperties); // overwrites parallelOnly!
}
}
fieldFitting.setCenterXY(currentPX0,currentPY0);
if (setupMasks) {
if (!fieldFitting.maskSetDialog("Setup parameter masks")) return false;
}
if (setupParameters) {
if (!fieldFitting.showModifyParameterValues("Setup parameter values",showDisabled)) return false;
}
double [] centerXY=fieldFitting.getCenterXY();
currentPX0=centerXY[0];
currentPY0=centerXY[1];
this.savedVector=fieldFitting.createParameterVector(sagittalMaster);
// initialVector
return true;
if (setupMasks) {
if (!fieldFitting.maskSetDialog("Setup parameter masks")) return false;
} else {
fieldFitting.initSampleCorrChnParIndex(flattenSampleCoord());
}
if (setupParameters) {
if (!fieldFitting.showModifyParameterValues("Setup parameter values",showDisabled)) return false;
}
double [] centerXY=fieldFitting.getCenterXY();
currentPX0=centerXY[0];
currentPY0=centerXY[1];
this.savedVector=fieldFitting.createParameterVector(sagittalMaster);
// initialVector
return true;
}
private boolean [] dataWeightsToBoolean(){
......@@ -1007,17 +1046,30 @@ private boolean [] filterByValue (
true, // boolean corrected,
true //boolean allChannels
);
if (scale>1.0){
for (int chn=0;chn<fwhm.length;chn++) for (int sample=0;sample<fwhm[chn].length;sample++){
fwhm[chn][sample]*=scale;
}
} else {
if (zRanges==null) {
System.out.println("filterByValue(): scale <=1.0 and zRanges==null -> nothing filtered");
return enable_in.clone();
}
for (int chn=0;chn<fwhm.length;chn++) for (int sample=0;sample<fwhm[chn].length;sample++){
if ((zRanges[chn]!=null) && (zRanges[chn][sample]!=null)){
fwhm[chn][sample]+=scale*(zRanges[chn][sample][2]-fwhm[chn][sample]); // based on worst accepted during calibration
}
}
}
int numFiltered=0;
// int numLeft=0;
if (scale>0.0) {
for (int index=0;index<dataVector.length;index++) if ((index>=enable_masked.length) || enable_masked[index]){
int chn=dataVector[index].channel;
int sample=dataVector[index].sampleIndex;
if (dataVector[index].value > scale*fwhm[chn][sample]){
if (dataVector[index].value > fwhm[chn][sample]){
enable_out[index]=false;
numFiltered++;
// } else {
// numLeft++;
}
}
}
......@@ -1458,6 +1510,120 @@ private boolean [] filterCrazyInput(
return enable_out;
}
private boolean [] filterSets(
boolean [] enable_in,
double scaleRMS,
boolean [] scanMask // if not null, will not touch samples where true
){
double [] sv=fieldFitting.createParameterVector(sagittalMaster);
double [] fX= createFXandJacobian(sv, false);
double maxRMS= scaleRMS*calcErrorDiffY(fX, true);
int [] indices=getSetIndices();
double [] setRMA=calcErrorsPerSet(fX);
if (enable_in==null) {
enable_in=new boolean [dataVector.length];
for (int i=0;i<enable_in.length;i++)enable_in[i]=true;
}
boolean [] enable_masked=enable_in.clone();
if (scanMask!=null) {
for (int i=0;i<enable_masked.length;i++) if ((i<scanMask.length) && scanMask[i]) enable_masked[i]=false;
}
boolean [] enable_out=enable_masked.clone();
int numFiltered=0;
for (int numSet=0;numSet<setRMA.length;numSet++) if (setRMA[numSet]>maxRMS){
int nextIndex=(numSet==(indices.length-1)?dataVector.length:indices[numSet+1]);
for (int i=indices[numSet];i<nextIndex;i++) if (enable_out[i]){
numFiltered++;
enable_out[i]=false;
}
}
// restore masked out data
if (scanMask!=null) {
for (int i=0;i<enable_out.length;i++) if (
(i<scanMask.length) &&
scanMask[i] &&
enable_in[i]) enable_out[i]=true;
}
if (debugLevel>0) {
int numLeft=0;
for (int i=0;i<enable_out.length;i++) if (enable_out[i]) numLeft++;
System.out.println("filterSets(): Filtered "+numFiltered+" samples, left "+numLeft+" samples");
}
return enable_out;
}
private boolean [] filterLowNeighbors(
boolean [] enable_in, // [meas][cjn][sample] (or null) // can be shorter or longer than dataVector
int minNeib,
boolean calibMode
){
if (enable_in==null) {
enable_in=new boolean [dataVector.length];
for (int i=0;i<enable_in.length;i++)enable_in[i]=true;
}
boolean [] enable_out=enable_in.clone();
boolean [][] usedSamples=new boolean[getNumChannels()][getNumSamples()];
int height=sampleCoord.length;
int width= sampleCoord[0].length;
int numFiltered=0;
int lastIndex;
int firstIndex;
int nextIndex=0;
String lastTimestamp="";
int [][]dirs={{1,0},{1,1},{0,1},{-1,1},{-1,0},{-1,-1},{0,-1},{1,-1}};
while (nextIndex < dataVector.length){
// find first enabled sample
for(firstIndex=nextIndex;(firstIndex<dataVector.length) && ((firstIndex < enable_in.length) && !enable_in[firstIndex]); firstIndex++);
// if (firstIndex>=dataVector.length){
// break;
// }
lastTimestamp=dataVector[firstIndex].timestamp;
lastIndex=firstIndex;
for (nextIndex=firstIndex; nextIndex<dataVector.length; nextIndex++) if ((nextIndex >= enable_in.length) || enable_in[nextIndex]){
if (dataVector[nextIndex].timestamp.equals(lastTimestamp)) lastIndex=nextIndex;
else break;
}
for (int chn=0;chn<usedSamples.length;chn++) for (int sample=0;sample<usedSamples[chn].length;sample++) usedSamples[chn][sample]=false;
for (int index=firstIndex;index<=lastIndex;index++) if ((index >= enable_in.length) || enable_in[index]){
usedSamples[dataVector[index].channel][dataVector[index].sampleIndex]=true;
}
for (int chn=0;chn<usedSamples.length;chn++){
boolean removed;
do {
removed=false;
boolean [] left=usedSamples[chn].clone();
for (int y=0;y<height;y++) for (int x=0;x<width;x++) if (usedSamples[chn][y*width+x]){
int n=0;
for (int d=0;d<dirs.length;d++){
int [] dXY=dirs[d].clone();
if (((x==0) && (dXY[0]<0)) || ((x==(width-1)) && (dXY[0]>0))) dXY[0]=-dXY[0];
if (((y==0) && (dXY[1]<0)) || ((y==(height-1)) && (dXY[1]>0))) dXY[1]=-dXY[1];
if (usedSamples[chn][(y+dXY[1])*width+(x+dXY[0])]) n++;
}
if (n<minNeib){
removed=true;
left[y*width+x]=false;
}
}
usedSamples[chn]=left.clone();
} while (removed);
}
for (int index=firstIndex;index<=lastIndex;index++) if ((index >= enable_in.length) || enable_in[index]){
if (!usedSamples[dataVector[index].channel][dataVector[index].sampleIndex]){
numFiltered++;
enable_out[index]=false;
};
}
}
if (debugLevel+(calibMode?1:0)>1) {
int numLeft=0;
for (int i=0;i<enable_out.length;i++) if (enable_out[i]) numLeft++;
System.out.println("filterLowNeighbors("+minNeib+"): Filtered "+numFiltered+" samples, left "+numLeft+" samples");
}
return enable_out;
}
private int [] getParallelDiff(MeasuredSample [] vector){
HashMap<Point,AtomicInteger> map=new HashMap<Point,AtomicInteger>();
......@@ -1618,6 +1784,25 @@ public void setDataVector(
maskDataWeights(en);
}
if (calibrateMode && (filterCalibByNeib>0)){
boolean [] en=dataWeightsToBoolean();
en= filterLowNeighbors(
en,
filterCalibByNeib,
true); // calibrate mode - for debug print
maskDataWeights(en);
}
if (calibrateMode && (filterSetsByRMS>0)){
boolean [] en=dataWeightsToBoolean();
en= filterSets(
en,
filterSetsByRMS,
filterSetsByRMSTiltOnly?scanMask:null);
maskDataWeights(en);
}
// TODO: add filtering for tilt motor calibration
fieldFitting.initSampleCorrVector(
......@@ -2264,8 +2449,62 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
}
return Math.sqrt(result);
}
public void printSetRMS(double [] fX){
int [] indices=getSetIndices();
double [] setRMA=calcErrorsPerSet(fX);
for (int numSet=0;numSet<indices.length;numSet++){
System.out.println(numSet+" "+IJ.d2s(setRMA[numSet],3)+" "+
dataVector[indices[numSet]].motors[0]+":"+dataVector[indices[numSet]].motors[1]+":"+dataVector[indices[numSet]].motors[2]+" "+
dataVector[indices[numSet]].timestamp);
}
}
public double [] calcErrorsPerSet(double [] fX){
int [] indices=getSetIndices();
double [] setRMA=new double[indices.length];
double [] weights=this.dataWeights;
if (weights==null){
weights=new double [fX.length];
for (int i=0;i<weights.length;i++) weights[i]=1.0;
}
for (int numSet=0;numSet<indices.length;numSet++){
int nextIndex=(numSet==(indices.length-1)?dataVector.length:indices[numSet+1]);
double result=0;
double sumWeights=0;
for (int i=indices[numSet];i<nextIndex;i++){
double diff=this.dataValues[i]-fX[i];
result+=diff*diff*weights[i];
sumWeights+=weights[i];
}
if (sumWeights>0) result/=sumWeights;
setRMA[numSet]=Math.sqrt(result);
}
return setRMA;
}
public int [] getSetIndices(){
String lastTimestamp="";
int numMeas=0;
for (int i=0;i<dataVector.length;i++){
if (!dataVector[i].timestamp.equals(lastTimestamp)){
lastTimestamp=dataVector[i].timestamp;
numMeas++;
}
}
int [] indices= new int [numMeas];
numMeas=0;
for (int i=0;i<dataVector.length;i++){
if (!dataVector[i].timestamp.equals(lastTimestamp)){
lastTimestamp=dataVector[i].timestamp;
indices[numMeas++]=i;
}
}
return indices;
}
public LMAArrays calculateJacobianArrays(double [] fX){
// calculate JtJ
double [] diff=calcYminusFx(fX);
......@@ -3510,6 +3749,7 @@ public double getAdjustRMS(
boolean filterZ,
boolean filterByScanValue,
double filterByValueScale,
int minNeib,
double z,
double tx,
double ty){
......@@ -3552,6 +3792,15 @@ public double getAdjustRMS(
int numEn=getNumEnabledSamples(en);
if (numEn<minLeftSamples) return Double.NaN;
}
if (minNeib>0){
boolean [] en=dataWeightsToBoolean();
en= filterLowNeighbors(
en,
minNeib,
false); // calib mode for debug print
maskDataWeights(en);
}
if ((minCenterSamplesTotal>0) || (minCenterSamplesBest>0)){
boolean [] centerSampesMask= getCenterSamples(centerSamples);
boolean [] en=dataWeightsToBoolean();
......@@ -3560,7 +3809,7 @@ public double getAdjustRMS(
en,
minCenterSamplesTotal, //int minTotalSamples,
minCenterSamplesBest )){ //int minBestChannelSamples)){
if (debugLevel>0) {
if (debugLevel>1) { //0
int [] numSamples=getNumCenterSamples( // per channel
centerSampesMask,
en);
......@@ -3584,6 +3833,7 @@ public double [] findAdjustZ(
boolean filterZ,
boolean filterByScanValue,
double filterByValueScale,
int minNeib,
double zMin,
double zMax,
double zStep,
......@@ -3601,6 +3851,7 @@ public double [] findAdjustZ(
filterZ,
filterByScanValue,
filterByValueScale,
minNeib,
z,
tx,
ty);
......@@ -3713,6 +3964,14 @@ public boolean LevenbergMarquardt(
int numEn=getNumEnabledSamples(en);
if (numEn<minLeftSamples) return false;
}
if (filterByNeib>0){
boolean [] en=dataWeightsToBoolean();
en= filterLowNeighbors(
en,
filterByNeib,
false); // calibrate mode - for debug print
maskDataWeights(en);
}
if ((minCenterSamplesTotal>0) || (minCenterSamplesBest>0)){
boolean [] centerSampesMask= getCenterSamples(centerSamples);
......@@ -3726,10 +3985,9 @@ public boolean LevenbergMarquardt(
int [] numSamples=getNumCenterSamples( // per channel
centerSampesMask,
en);
System.out.println("Not enough center samples, requested "+minCenterSamplesBest+" best channel and "+minCenterSamplesTotal+" total.");
System.out.print("Got:");
System.out.print("Got (in LMA):");
for (int n:numSamples) System.out.print(" "+n);
System.out.println();
System.out.println(" - not enough center samples, requested "+minCenterSamplesBest+" best channel and "+minCenterSamplesTotal+" total.");
}
return false;
}
......@@ -4166,6 +4424,7 @@ public boolean LevenbergMarquardt(
gd.addCheckbox("Filter samples/channels by Z",filterZ);
gd.addCheckbox("Filter by value (leave lower than maximal fwhm used in focal scan mode)",filterByScanValue);
gd.addNumericField("Filter by value (remove samples above scaled best FWHM for channel/location)",filterByValueScale,2,5,"x");
gd.addNumericField("Remove samples having less neighbors (same channel) that this during ",filterByNeib,0,1,"");
gd.addNumericField("Minimal required number of channels/samples",minLeftSamples,0,3,"samples");
gd.addNumericField("... of them closest to the center, best channel",minCenterSamplesBest,0,3,"samples");
gd.addNumericField("... of them closest to the center, total in all channels",minCenterSamplesTotal,0,3,"samples");
......@@ -4188,30 +4447,32 @@ public boolean LevenbergMarquardt(
gd.showDialog();
if (gd.wasCanceled()) return;
nMeas=(int) gd.getNextNumber();
nMeas=(int) gd.getNextNumber();
for (int i=0;i<fieldFitting.channelSelect.length;i++) {
fieldFitting.channelSelect[i]=gd.getNextBoolean();
}
filterZ= gd.getNextBoolean();
filterByScanValue= gd.getNextBoolean();
filterByValueScale=gd.getNextNumber();
minLeftSamples=(int) gd.getNextNumber();
minCenterSamplesBest=(int) gd.getNextNumber();
minCenterSamplesTotal=(int) gd.getNextNumber();
centerSamples=(int) gd.getNextNumber();
maxRMS=gd.getNextNumber();
zMin= gd.getNextNumber();
zMax= gd.getNextNumber();
zStep=gd.getNextNumber();
tMin= gd.getNextNumber();
tMax= gd.getNextNumber();
tStep=gd.getNextNumber();
targetRelFocalShift=gd.getNextNumber();
targetTiltX=gd.getNextNumber(); // for testing, normally should be 0 um/mm
targetTiltY=gd.getNextNumber(); // for testing, normally should be 0 um/mm
filterZ= gd.getNextBoolean();
filterByScanValue= gd.getNextBoolean();
filterByValueScale= gd.getNextNumber();
filterByNeib= (int) gd.getNextNumber();
minLeftSamples= (int) gd.getNextNumber();
minCenterSamplesBest= (int) gd.getNextNumber();
minCenterSamplesTotal= (int) gd.getNextNumber();
centerSamples= (int) gd.getNextNumber();
maxRMS= gd.getNextNumber();
zMin= gd.getNextNumber();
zMax= gd.getNextNumber();
zStep= gd.getNextNumber();
tMin= gd.getNextNumber();
tMax= gd.getNextNumber();
tStep= gd.getNextNumber();
targetRelFocalShift= gd.getNextNumber();
targetTiltX= gd.getNextNumber(); // for testing, normally should be 0 um/mm
targetTiltY= gd.getNextNumber(); // for testing, normally should be 0 um/mm
boolean OK;
fieldFitting.mechanicalFocusingModel.setAdjustMode(true); // to correctly find Z centers,
......@@ -4231,6 +4492,8 @@ public boolean LevenbergMarquardt(
boolean single= (nMeas>=0);
if (single){
if (debugLevel>0) System.out.print("======== testMeasurement("+nMeas+") ======== ");
OK=testMeasurement(
measurements.get(nMeas),
// nMeas,
......@@ -4241,11 +4504,13 @@ public boolean LevenbergMarquardt(
tMax,
tStep
);
if ((debugLevel>0)&& (dataVector.length>0)){
System.out.println("Motors= "+dataVector[0].motors[0]+" : "+ dataVector[0].motors[1]+" : "+dataVector[0].motors[2]+" timestamp= "+dataVector[0].timestamp);
}
if (!OK){
if (debugLevel>0) System.out.println("testMeasurement("+nMeas+") failed");
} else {
if (debugLevel>0) System.out.print("======== testMeasurement("+nMeas+") ========");
if (debugLevel>0) System.out.println(showSamples());
for (int i=0;i<fieldFitting.mechanicalFocusingModel.paramValues.length;i++){
if ((fieldFitting.mechanicalSelect==null) || fieldFitting.mechanicalSelect[i] ) {
System.out.println(
......@@ -4293,7 +4558,7 @@ public boolean LevenbergMarquardt(
}
} else {
for (nMeas=0;nMeas<measurements.size();nMeas++){
if (debugLevel>0) System.out.print("======== testMeasurement("+nMeas+") ======== ");
if (debugLevel>0) System.out.print("======== testMeasurement("+nMeas+") ======== ");
OK=testMeasurement(
measurements.get(nMeas),
zMin, //+best_qb_corr[0],
......@@ -4302,9 +4567,13 @@ public boolean LevenbergMarquardt(
tMin,
tMax,
tStep);
if ((debugLevel>0)&& (dataVector.length>0)){
System.out.println("Motors= "+dataVector[0].motors[0]+" : "+ dataVector[0].motors[1]+" : "+dataVector[0].motors[2]+" timestamp= "+dataVector[0].timestamp);
}
if (!OK){
if (debugLevel>0) System.out.println("testMeasurement("+nMeas+") failed");
} else {
if (debugLevel>0) System.out.println(showSamples());
for (int i=0;i<fieldFitting.mechanicalFocusingModel.paramValues.length;i++){
if ((fieldFitting.mechanicalSelect==null) || fieldFitting.mechanicalSelect[i] ) {
System.out.println(
......@@ -4373,6 +4642,28 @@ public boolean LevenbergMarquardt(
}
//,
public String showSamples(){
boolean [][] usedSamples=new boolean[getNumChannels()][getNumSamples()];
for (int chn=0;chn<usedSamples.length;chn++) for (int sample=0;sample<usedSamples[chn].length;sample++) usedSamples[chn][sample]=false;
for (int i=0;i<dataVector.length;i++) if (dataWeights[i]>0.0){
usedSamples[dataVector[i].channel][dataVector[i].sampleIndex]=true;
}
int height=sampleCoord.length;
int width= sampleCoord[0].length;
String s="";
for (int i=0;i<height;i++){
for (int chn=0;chn<usedSamples.length;chn++){
for (int j=0;j<width;j++){
s+=usedSamples[chn][i*width+j]?"+":".";
s+=" ";
}
if (chn<(usedSamples.length-1)) s+=" ";
}
s+="\n";
}
return s;
}
public double [][] getAllZTM(
boolean noTiltScan,
FocusingField ff){
......@@ -4511,6 +4802,7 @@ public boolean LevenbergMarquardt(
filterZ, //boolean filterZ,
filterByScanValue,
filterByValueScale,
filterByNeib,
zMin,
zMax,
zStep,
......@@ -4533,10 +4825,8 @@ public boolean LevenbergMarquardt(
boolean OK=LevenbergMarquardt(
measurement,
false, // true, // open dialog
// filterZ, // filterZ
debugLevel);
if (!OK){
// if (debugLevel>0) System.out.println("testMeasurement("+nMeas+") failed");
if (debugLevel>1) System.out.println("testMeasurement() failed: LMA failed");
return false;
}
......
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